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Project

Integrating molecular archeology and Bayesian phylodynamics to elucidate the hidden history of HIV-1.

Combating pathogen spread and its associated disease burden is a tremendous challenge requiring sustained research efforts and decided public health measures. The availability of genomic data provides a major asset in characterizing the interplay between viral evolution and host ecological dynamics, including the determination of the key factors for successful epidemic spread in the human population. These factors are, however, still largely obscure for one of the most devastating pandemics in human history, the AIDS pandemic caused by Human Immunodeficiency Viruses (HIV). Despite continual developments in the field of statistical phylodynamics, historical inferences based on contemporaneous sequence data have inherent limitations. Motivated by the possibility to inform such analyses with HIV-1 sequences recovered from archival histopathological specimens, we here propose to create a panel of fossil HIV sequences using state-of-the-art sequencing technology based on a u nique, invaluable and comprehensive library of archival samples (n = ~31.500) collected between 1955 and 1980 from different locations in Central Africa, in particular the Democratic Republic of Congo. We will complement the wet-lab efforts by advancing phylogenetic reconstruction methodology to refine time-estimates for the origin of HIV-1 group M, and to reconstruct the dynamics in viral population size and spatial expansion over time. This will allow us to explicitly test different hypotheses about the emergence and early epidemic onset of HIV-1 group M. More broadly, our research can open up new opportunities for uncovering the past history of other fast-evolving viruses and stimulate viral discovery research.
Date:1 Oct 2014 →  30 Sep 2018
Keywords:Phylogenetics, Evolution, Phylodynamics, HIV
Disciplines:Scientific computing, Bioinformatics and computational biology, Public health care, Public health services, Microbiology, Systems biology, Laboratory medicine, Public health sciences